RegulonDB RegulonDB 11.1: Gene Form
   

pdxJ gene in Escherichia coli K-12 genome


Gene local context to scale (view description)

pdxJ recO acpS ohsC TSS_2857 TSS_2857 TSS_2856 TSS_2856 pdxJp pdxJp acpSp3 acpSp3 acpSp2 acpSp2

Gene      
Name: pdxJ    Texpresso search in the literature
Synonym(s): ECK2562, EG10693, b2564
Genome position(nucleotides): 2700998 <-- 2701729
Strand: reverse
Sequence: Get nucleotide sequence FastaFormat
GC content %:  
 56.42
External database links:  
ASAP:
 ABE-0008435
CGSC:
 416
ECHOBASE:
 EB0687
ECOLIHUB:
 pdxJ
NCBI-GENE:
 947039
OU-MICROARRAY:
 b2564
STRING:
 511145.b2564
COLOMBOS: pdxJ


Product      
Name: pyridoxine 5'-phosphate synthase
Synonym(s): PdxJ
Sequence: Get amino acid sequence Fasta Format
Cellular location: cytosol
Molecular weight: 26.384
Isoelectric point: 5.817
Motif(s):
 
Type Positions Sequence Comment
2 -> 243 AELLLGVNIDHIATLRNARGTAYPDPVQAAFIAEQAGADGITVHLREDRRHITDRDVRILRQTLDTRMNLEMAVTEEMLAIAVETKPHFCCLVPEKRQEVTTEGGLDVAGQRDKMRDACKRLADAGIQVSLFIDADEEQIKAAAEVGAPFIEIHTGCYADAKTDAEQAQELARIAKAATFAASLGLKVNAGHGLTYHNVKAIAAIPEMHELNIGHAIIGRAVMTGLKDAVAEMKRLMLEARG UniProt: Pyridoxine 5'-phosphate synthase.
6 -> 238 LGVNIDHIATLRNARGTAYPDPVQAAFIAEQAGADGITVHLREDRRHITDRDVRILRQTLDTRMNLEMAVTEEMLAIAVETKPHFCCLVPEKRQEVTTEGGLDVAGQRDKMRDACKRLADAGIQVSLFIDADEEQIKAAAEVGAPFIEIHTGCYADAKTDAEQAQELARIAKAATFAASLGLKVNAGHGLTYHNVKAIAAIPEMHELNIGHAIIGRAVMTGLKDAVAEMKRLM
11 -> 12 DH UniProt: 1-deoxy-D-xylulose 5-phosphate binding; Sequence Annotation Type: region of interest.
194 -> 194 G UniProt: In pdxH null mutation suppressor..
215 -> 216 GH UniProt: 3-amino-2-oxopropyl phosphate binding; Sequence Annotation Type: region of interest.

 
Classification:
Multifun Terms (GenProtEC)  
  1 - metabolism --> 1.5 - biosynthesis of building blocks --> 1.5.3 - cofactors, small molecule carriers --> 1.5.3.6 - pyridoxal 5'phosphate
Gene Ontology Terms (GO)  
cellular_component GO:0005737 - cytoplasm
GO:0005829 - cytosol
molecular_function GO:0003824 - catalytic activity
GO:0016740 - transferase activity
GO:0016769 - transferase activity, transferring nitrogenous groups
GO:0042802 - identical protein binding
GO:0033856 - pyridoxine 5'-phosphate synthase activity
biological_process GO:0008615 - pyridoxine biosynthetic process
Note(s): Note(s): ...[more].
Reference(s): [1] Man TK., et al., 1996
[2] Matsunaga J., et al., 1996
[3] Sakai A., et al., 2004
[4] Wetzel DK., et al., 2004
External database links:  
ALPHAFOLD:
 P0A794
DIP:
 DIP-36215N
ECOCYC:
 PDXJ-MONOMER
ECOLIWIKI:
 B2564
INTERPRO:
 IPR013785
INTERPRO:
 IPR036130
INTERPRO:
 IPR004569
MODBASE:
 P0A794
PANTHER:
 PTHR30456
PDB:
 1IXN
PDB:
 1IXO
PDB:
 6RG0
PDB:
 1HO4
PDB:
 1IXQ
PDB:
 1M5W
PDB:
 1HO1
PDB:
 1IXP
PFAM:
 PF03740
PRIDE:
 P0A794
PRODB:
 PRO_000023505
REFSEQ:
 NP_417059
SMR:
 P0A794
UNIPROT:
 P0A794


Operon      
Name: rnc-era-recO-pdxJ-acpS         
Operon arrangement:
Transcription unit        Promoter
pdxJ-acpS
rnc-era
rnc-era-recO-pdxJ-acpS


Elements in the selected gene context region unrelated to any object in RegulonDB      

  Type Name Post Left Post Right Strand Notes Evidence (Confirmed, Strong, Weak) References
  promoter acpSp2 2701137 reverse nd [COMP-AINF] [5]
  promoter acpSp3 2701162 reverse nd [COMP-AINF] [5]
  promoter TSS_2856 2702292 reverse nd [RS-EPT-CBR] [6]
  promoter TSS_2857 2702302 reverse nd [RS-EPT-CBR] [6]


Evidence    

 [COMP-AINF] Inferred computationally without human oversight

 [RS-EPT-CBR] RNA-seq using two enrichment strategies for primary transcripts and consistent biological replicates


Reference(s)    

 [1] Man TK., Zhao G., Winkler ME., 1996, Isolation of a pdxJ point mutation that bypasses the requirement for the PdxH oxidase in pyridoxal 5' -phosphate coenzyme biosynthesis in Escherichia coli K-12., J Bacteriol 178(8):2445-9

 [2] Matsunaga J., Dyer M., Simons EL., Simons RW., 1996, Expression and regulation of the rnc and pdxJ operons of Escherichia coli., Mol Microbiol 22(5):977-89

 [3] Sakai A., Kita M., Tani Y., 2004, Recent progress of vitamin B6 biosynthesis., J Nutr Sci Vitaminol (Tokyo) 50(2):69-77

 [4] Wetzel DK., Ehrenshaft M., Denslow SA., Daub ME., 2004, Functional complementation between the PDX1 vitamin B6 biosynthetic gene of Cercospora nicotianae and pdxJ of Escherichia coli., FEBS Lett 564(1-2):143-6

 [5] Huerta AM., Collado-Vides J., 2003, Sigma70 promoters in Escherichia coli: specific transcription in dense regions of overlapping promoter-like signals., J Mol Biol 333(2):261-78

 [6] Salgado H, Peralta-Gil M, Gama-Castro S, Santos-Zavaleta A, Muñiz-Rascado L, García-Sotelo JS, Weiss V, Solano-Lira H, Martínez-Flores I, Medina-Rivera A, Salgado-Osorio G, Alquicira-Hernández S, Alquicira-Hernández K, López-Fuentes A, Porrón-Sotelo L, Huerta AM, Bonavides-Martínez C, Balderas-Martínez YI, Pannier L, Olvera M, Labastida A, Jiménez-Jacinto V, Vega-Alvarado L, Del Moral-Chávez V, Hernández-Alvarez A, Morett E, Collado-Vides J., 2012, RegulonDB v8.0: omics data sets, evolutionary conservation, regulatory phrases, cross-validated gold standards and more., Nucleic Acids Res.

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